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MDL rarely used patents and chose to protect its technology using trade secrets. A patent grants a monopoly for a limited time but requires that the nature of the invention must be fully disclosed, whereas there is no time limit on the protection offered by a trade secret.

A patent discloses the nature of the invention. This may spur other inventors to new inventions that do no infringe the original patent. Drugs are a good example. Rarely does a novel drug exit for long without competitors; examples are: cimetidine and ranitidine, sildenafil and vardenafil. Trade secrets enable inventions to be concealed indefinitely; the formula for Coca Cola® remains a closely guarded secret since its introduction in 1886. Others have tried to copy the formula but none is identical to the original.

If it is possible to determine the nature of the invention by examination of the invention, then it should be protected by a patent. Software inventions are well suited to protection using trade secrets because the nature of the invention usually cannot be determined by examination of the compiled code.

MDL's reliance on trade secrets means that there is very little published on how their products worked. Following the absorption of MDL into Symyx, then Accelrys (now BIOVIA) many of the original inventors left taking the knowledge with them. This has created a hiatus in the evolution of chemical structure handling that is slowly being filled as other companies independently discover MDL's trade secrets.

More detail on how patents and trade secrets protect intellectual property can be found in Wikipedia.